Search for Variation information by Variation ID:
Detailed information for vg1118146962:
| Variant ID: vg1118146962 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 18146962 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 268. )
Flanking Sequence (100 bp) in Reference Genome:
TTGCGTAGAATTTATCGAAGATCTTCGCCCAATCGGGATACCTGAATCACGCCATGAAGGGAGACTACGGGGAAAGGGAACTCTCGGAAGGAAAGCAATA[A/G]
TGACAGTAGACAACAATTTATTCCGTAAAGCCCATTCCACGGTTCTGCAACAATCTTCATTGGTAGCTCCTTACATCGAGGAGCACTTTGGCTCTAGTTC
Reverse complement sequence
GAACTAGAGCCAAAGTGCTCCTCGATGTAAGGAGCTACCAATGAAGATTGTTGCAGAACCGTGGAATGGGCTTTACGGAATAAATTGTTGTCTACTGTCA[T/C]
TATTGCTTTCCTTCCGAGAGTTCCCTTTCCCCGTAGTCTCCCTTCATGGCGTGATTCAGGTATCCCGATTGGGCGAAGATCTTCGATAAATTCTACGCAA
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 85.50% | 3.20% | 3.72% | 7.60% | NA |
| All Indica | 2759 | 86.10% | 5.40% | 5.26% | 3.23% | NA |
| All Japonica | 1512 | 82.10% | 0.10% | 0.60% | 17.20% | NA |
| Aus | 269 | 97.80% | 0.00% | 1.49% | 0.74% | NA |
| Indica I | 595 | 62.90% | 19.00% | 15.80% | 2.35% | NA |
| Indica II | 465 | 88.60% | 0.00% | 1.29% | 10.11% | NA |
| Indica III | 913 | 98.90% | 0.10% | 0.44% | 0.55% | NA |
| Indica Intermediate | 786 | 87.30% | 4.60% | 5.22% | 2.93% | NA |
| Temperate Japonica | 767 | 96.60% | 0.00% | 0.13% | 3.26% | NA |
| Tropical Japonica | 504 | 53.80% | 0.00% | 1.39% | 44.84% | NA |
| Japonica Intermediate | 241 | 95.40% | 0.40% | 0.41% | 3.73% | NA |
| VI/Aromatic | 96 | 84.40% | 0.00% | 15.62% | 0.00% | NA |
| Intermediate | 90 | 86.70% | 1.10% | 3.33% | 8.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1118146962 | A -> DEL | LOC_Os11g31160.1 | N | frameshift_variant | Average:37.698; most accessible tissue: Zhenshan97 panicle, score: 57.341 | N | N | N | N |
| vg1118146962 | A -> G | LOC_Os11g31160.1 | missense_variant ; p.Met225Val; MODERATE | nonsynonymous_codon ; M225V | Average:37.698; most accessible tissue: Zhenshan97 panicle, score: 57.341 | benign  |
0.945 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1118146962 | 4.73E-06 | 2.75E-06 | mr1800 | Ind_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |